There is another interesting approach which is http://livecode.com/  where code is generated from sort-of-natural-language statements. Maybe a semantic Wiktionary would be able to help there some day.
As for attaching physical effects to 3d entities, it has been done many times. The closest that comes to that modularity is Unity3d. Maybe not advanced enough for scientific purposes, but it is quite used for videogames.

Micru